This study aims to: (1) develop new markers for response to tuberculosis (TB) treatment through expression profiling or analysis of patterns of RNA expression in human blood as quantified by microarray technology and (2) determine whether small regulatory RNA (sRNA) secreted by M tuberculosis act to suppress expression of host-protective genes in macrophages through RNA interference (RNAi). New markers for response to TB treatment. Specific disease states may produce signature RNA patterns not seen in other conditions and the pathogen-specific component of human expression may distinguish between infections. Identifying expression that is specific to TB requires a clinically-relevant comparison group. To avoid over-estimating test accuracy, biomarkers should be developed in the patients likely to be tested in practice with an intention-to-test approach. The first step of this project will identify and validate a TB expression panel by comparison with patients with community-acquired pneumonia (CAP) in cohorts of subjects in the U.S. and Uganda. The second step will test whether expression of the TB panel in blood resolves with successful treatment of active TB. We hypothesize that expression of genes in the TB panel will change to resemble expression in controls without pneumonia, reflecting resolving immune response as bacillary burden decreases. Finally, it is unclear whether blood is a surrogate for understanding TB-specific responses in the lung. Although blood expression may identify effective biomarkers even without recapitulating lung expression, interpretation of the pathobiological significance of blood expression demands understanding the relationship between blood and lung expression. To determine the extent to which TB-specific expression in blood reflects inflammatory pathways in the lung this study will compare expression in simultaneously collected blood and BAL while adjusting for the different cell types present in each specimen type. sRNA secreted by Mtb may subvert host-protective macrophage responses via RNAi. RNAi, the biological process in which endogenous non-coding sRNA molecules bind mRNA and inhibit gene expression, is a fundamental regulatory mechanism in both Mtb and humans. sRNA secreted by Mtb was recently shown to increase bacterial viability in macrophages. We hypothesize that the mechanism for this increased viability is Mtb-derived sRNA silencing of expression of important human host-protective genes. Specifically, through RNA sequencing we have identified Mtb-derived sRNA which are predicted to bind the 3' untranslated region of key host-protective human mRNA transcripts for IkB, TRAF-3 and TRAF-5. We propose to validate this novel form of cross-species RNAi. If confirmed, this would represent a novel form of host-pathogen interaction that could offer new targets for anti-TB therapy.